Whole genome sequencing identifies a homozygous nonsense mutation in the JPH2 gene in Shih Tzu dogs with progressive retinal atrophy

2021 ◽  
Author(s):  
G. Urkasemsin ◽  
M. Pongpanich ◽  
L. Sariya ◽  
A. Kongcharoen ◽  
R. Buddhirongawatr ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Nonsense Mutation ◽  
Whole Genome ◽  
Progressive Retinal Atrophy ◽  
Retinal Atrophy ◽  
Homozygous Nonsense Mutation

scholarly journals Whole Genome Sequencing of Giant Schnauzer Dogs with Progressive Retinal Atrophy Establishes NECAP1 as a Novel Candidate Gene for Retinal Degeneration

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 385 ◽  
Author(s):  
Rebekkah J. Hitti ◽  
James A. C. Oliver ◽  
Ellen C. Schofield ◽  
Anina Bauer ◽  
Maria Kaukonen ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Whole Genome Sequencing ◽  
Retinal Degeneration ◽  
Genome Sequencing ◽  
Autosomal Recessive Disorder ◽  
Causal Variant ◽  
Whole Genome ◽  
Gene Encoding ◽  
Progressive Retinal Atrophy ◽  
Dna Test

Canine progressive retinal atrophies (PRA) are genetically heterogeneous diseases characterized by retinal degeneration and subsequent blindness. PRAs are untreatable and affect multiple dog breeds, significantly impacting welfare. Three out of seven Giant Schnauzer (GS) littermates presented with PRA around four years of age. We sought to identify the causal variant to improve our understanding of the aetiology of this form of PRA and to enable development of a DNA test. Whole genome sequencing of two PRA-affected full-siblings and both unaffected parents was performed. Variants were filtered based on those segregating appropriately for an autosomal recessive disorder and predicted to be deleterious. Successive filtering against 568 canine genomes identified a single nucleotide variant in the gene encoding NECAP endocytosis associated 1 (NECAP1): c.544G>A (p.Gly182Arg). Five thousand one hundred and thirty canids of 175 breeds, 10 cross-breeds and 3 wolves were genotyped for c.544G>A. Only the three PRA-affected GS were homozygous (allele frequency in GS, excluding proband family = 0.015). In addition, we identified heterozygotes belonging to Spitz and Dachshund varieties, demonstrating c.544G>A segregates in other breeds of German origin. This study, in parallel with the known retinal expression and role of NECAP1 in clathrin mediated endocytosis (CME) in synapses, presents NECAP1 as a novel candidate gene for retinal degeneration in dogs and other species.

Utility of Whole Genome Sequencing in diagnosing complex disorders: lesson from renal tubular disorders

2018 ◽  
Author(s):  
Mark Stevenson ◽  
Alistair T Pagnamenta ◽  
Heather G Mack ◽  
Judith A Savige ◽  
Kate E Lines ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Complex Disorders ◽  
Tubular Disorders ◽  
Renal Tubular Disorders ◽  
Renal Tubular

0306 Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments

2016 ◽  
Vol 94 (suppl_5) ◽  
pp. 146-146
Author(s):  
D. M. Bickhart ◽  
L. Xu ◽  
J. L. Hutchison ◽  
J. B. Cole ◽  
D. J. Null ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Copy Number ◽  
Large Scale ◽  
Copy Number Variants ◽  
Whole Genome

Evaluation of Whole Genome Sequencing for outbreak detection of Salmonella enterica serovar Enteritidis

2020 ◽  
Author(s):  
Ainhoa Arrieta-Gisasola ◽  
Aitor Atxaerandio Landa ◽  
Javier Garaizar ◽  
Joseba Bikandi ◽  
José Karkamo ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Outbreak Detection ◽  
Whole Genome ◽  
Salmonella Enterica Serovar Enteritidis
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